The purpose of this document is to test the back-calculated watershed areas. All code will be drawn from the IWAM function vignette.
The following function vignette/example is from the IWAM Package Repo hosted publicly through the Pacific Salmon Assess organization available at this link.
The package currently utilizes the following data sets:
IWAM_backcalc <- IWAM_func(WAin = "DataIn/Ordered_backcalculated_noagg.csv", # Data (INPUT)
# Ordered_backcalculated_noagg - ordered corrected to original input file
# Backcalc_targetstocks_NoAgg.csv - broken due to alphabetical ordering
remove.EnhStocks = FALSE, # Remove Enhancement stocks (INPUT)
run.bootstrap = TRUE, # TRUE/FALSE for running the bootstrap process
bs_seed = 1, # Change the internal seed for the bootstrap (INPUT)
bs_nBS = 20000, # Change the internal number of trials for the bootstrap (INPUT)
# Run 10 for testing purposes - otherwise 20000
plot = FALSE, # Print plots to DataOut/
est.table = FALSE # Store tables
)
This code is a direct lift from the IWAM function vignette. Once the model and bootstrapping has completed, the function will store the following objects:
dfout: A complete data frame containing the SGEN, SREP,
and SMSY estimates for each stock and their upper and lower
quantiles.The following tables (1-3) have been prepared for comparison to Holt et al. (2023) Res Doc (Table 9). The table will also be stored in your repository folder under the name of “Backcalculation_stockestimates_table.csv”.
Table 1. SGEN, SREP, and SMSY estimates including 0.25% and 97.5% quantiles for all listed stocks. Watershed areas are back-calculated from Parken estimates with the exception of all WCVI stocks, which use original watershed areas: Nahmint, Sarita, Somass, Bedwell/Ursus, Cypre, Megin, Moyeha, Tranquil, Artlish, Kaouk, Tahsish, Nitinat, Burman, Conuma, Gold, Leiner, Tahsis, Zeballos, Cayeghle, Marble, San Juan, Canton Creek, Espinosa, Kauwinch River, Kleeptee, Little Zeballos River, Malksope River, McKay Cove Creek, Mooyah River, Ououkinsh River, Sucwoa River, Tlupana River, Tsowwin River.
| Stock | WA | SGEN | SGEN LQ | SGEN UQ | SREP | SREP LQ | SREP UQ | SMSY | SMSY LQ | SMSY UQ |
|---|---|---|---|---|---|---|---|---|---|---|
| South Thompson Agg | 29565 | 94000 | 23000.00 | 320000 | 490000 | 230000 | 1000000 | 210000 | 99000.0 | 450000 |
| Lower Shuswap | 2663 | 8200 | 2100.00 | 25000 | 43000 | 24000 | 76000 | 18000 | 10000.0 | 33000 |
| Middle Shuswap | 640 | 2000 | 480.00 | 6000 | 10000 | 5700 | 18000 | 4400 | 2400.0 | 7800 |
| Wap | 20 | 57 | 13.00 | 210 | 300 | 130 | 710 | 130 | 53.0 | 310 |
| East | 46 | 130 | 32.00 | 470 | 710 | 330 | 1500 | 310 | 140.0 | 670 |
| Goodspeed | 15 | 41 | 9.20 | 160 | 220 | 88 | 540 | 94 | 37.0 | 240 |
| Keith | 56 | 160 | 38.00 | 560 | 860 | 400 | 1800 | 370 | 170.0 | 800 |
| Klaskish | 41 | 120 | 26.00 | 410 | 620 | 280 | 1400 | 270 | 120.0 | 590 |
| Mahatta | 114 | 340 | 80.00 | 1100 | 1800 | 890 | 3500 | 760 | 380.0 | 1500 |
| Washlawlis | 23 | 66 | 15.00 | 250 | 350 | 150 | 810 | 150 | 63.0 | 350 |
| Colonial&Cayeagle | 79 | 230 | 55.00 | 780 | 1200 | 590 | 2400 | 520 | 250.0 | 1100 |
| Marble | 168 | 500 | 120.00 | 1600 | 2600 | 1300 | 5000 | 1100 | 570.0 | 2200 |
| Adam | 279 | 830 | 210.00 | 2700 | 4400 | 2400 | 8000 | 1900 | 1000.0 | 3500 |
| Amor de Cosmos | 15 | 42 | 8.70 | 160 | 220 | 87 | 540 | 94 | 37.0 | 240 |
| Cluxewe | 90 | 260 | 62.00 | 870 | 1400 | 680 | 2800 | 600 | 290.0 | 1200 |
| Kokish | 104 | 310 | 74.00 | 1000 | 1600 | 810 | 3200 | 690 | 340.0 | 1400 |
| Quatse | 80 | 230 | 56.00 | 780 | 1200 | 600 | 2500 | 530 | 250.0 | 1100 |
| Nimpkish (above Lake) | 400 | 1200 | 300.00 | 3700 | 6300 | 3500 | 11000 | 2700 | 1500.0 | 5000 |
| Salmon | 912 | 2800 | 690.00 | 8400 | 15000 | 8200 | 26000 | 6300 | 3500.0 | 11000 |
| Quinsam-Campbell | 171 | 510 | 120.00 | 1600 | 2600 | 1400 | 5000 | 1100 | 580.0 | 2200 |
| Conuma | 20 | 57 | 12.00 | 210 | 300 | 130 | 720 | 130 | 53.0 | 310 |
| Tahsis | 77 | 230 | 54.00 | 760 | 1200 | 580 | 2500 | 510 | 250.0 | 1100 |
| Burman | 70 | 210 | 48.00 | 690 | 1100 | 520 | 2200 | 460 | 220.0 | 970 |
| Artlish | 64 | 190 | 44.00 | 630 | 970 | 460 | 2000 | 420 | 200.0 | 890 |
| Kaouk | 101 | 300 | 71.00 | 990 | 1600 | 780 | 3100 | 670 | 330.0 | 1400 |
| Tahsish | 172 | 520 | 120.00 | 1600 | 2700 | 1400 | 5100 | 1200 | 590.0 | 2200 |
| Gold | 856 | 2600 | 680.00 | 7800 | 14000 | 7800 | 24000 | 5900 | 3300.0 | 10000 |
| Leiner | 109 | 330 | 78.00 | 1100 | 1700 | 860 | 3300 | 730 | 360.0 | 1500 |
| Zeballos | 194 | 580 | 140.00 | 1800 | 3000 | 1600 | 5700 | 1300 | 680.0 | 2500 |
| Amai | 14 | 39 | 8.20 | 150 | 210 | 81 | 510 | 88 | 35.0 | 220 |
| Canton | 10 | 28 | 5.90 | 110 | 150 | 57 | 380 | 63 | 24.0 | 160 |
| Espinosa | 5 | 13 | 2.50 | 58 | 70 | 24 | 200 | 30 | 10.0 | 89 |
| Hoiss | 13 | 38 | 8.20 | 150 | 200 | 81 | 500 | 87 | 34.0 | 220 |
| Kauwinch | 44 | 130 | 29.00 | 450 | 670 | 310 | 1400 | 290 | 130.0 | 630 |
| Kleeptee | 14 | 40 | 8.80 | 150 | 210 | 85 | 520 | 90 | 36.0 | 230 |
| Little Zeballos River | 43 | 130 | 29.00 | 440 | 660 | 310 | 1500 | 280 | 130.0 | 640 |
| Malksope | 20 | 59 | 13.00 | 220 | 310 | 130 | 740 | 130 | 55.0 | 320 |
| Mckay | 1 | 4 | 0.68 | 20 | 21 | 6 | 75 | 9 | 2.6 | 32 |
| Mooyah | 8 | 22 | 4.40 | 88 | 120 | 43 | 310 | 50 | 18.0 | 140 |
| Ououkinsh | 17 | 47 | 10.00 | 180 | 250 | 100 | 620 | 110 | 43.0 | 270 |
| Power | 51 | 150 | 34.00 | 500 | 780 | 360 | 1700 | 340 | 150.0 | 730 |
| Sucwoa | 25 | 75 | 17.00 | 270 | 390 | 170 | 890 | 170 | 72.0 | 390 |
| Tlupana | 20 | 57 | 12.00 | 220 | 300 | 130 | 720 | 130 | 53.0 | 310 |
| Tsowwin | 26 | 75 | 16.00 | 270 | 400 | 170 | 910 | 170 | 73.0 | 400 |
| Nitinat | 357 | 1100 | 270.00 | 3300 | 5600 | 3000 | 10000 | 2400 | 1300.0 | 4500 |
| San Juan | 330 | 990 | 250.00 | 3000 | 5200 | 2800 | 9400 | 2200 | 1200.0 | 4100 |
| Nahmint | 42 | 120 | 28.00 | 420 | 640 | 290 | 1400 | 270 | 120.0 | 610 |
| Sarita | 84 | 250 | 59.00 | 830 | 1300 | 630 | 2700 | 560 | 270.0 | 1200 |
| Bedwell | 99 | 290 | 71.00 | 940 | 1500 | 780 | 3000 | 660 | 330.0 | 1300 |
| Megin | 245 | 730 | 180.00 | 2300 | 3800 | 2100 | 7100 | 1600 | 870.0 | 3100 |
| Moyeha | 116 | 340 | 83.00 | 1100 | 1800 | 900 | 3500 | 770 | 380.0 | 1500 |
| Cypre | 39 | 110 | 26.00 | 400 | 590 | 270 | 1300 | 250 | 110.0 | 570 |
| Tranquil | 12 | 35 | 7.40 | 130 | 180 | 74 | 460 | 79 | 31.0 | 200 |
| Somass (stamp&sproat) | 1057 | 3200 | 810.00 | 9800 | 17000 | 9600 | 30000 | 7200 | 4000.0 | 13000 |
| Puntledge Falls | 560 | 1700 | 430.00 | 5200 | 8800 | 5000 | 16000 | 3800 | 2100.0 | 6900 |
| Englishman | 299 | 890 | 220.00 | 2800 | 4700 | 2600 | 8500 | 2000 | 1100.0 | 3800 |
| Big Qualicum | 137 | 400 | 98.00 | 1300 | 2100 | 1100 | 4100 | 920 | 460.0 | 1800 |
| Little Qualicum | 95 | 280 | 66.00 | 910 | 1500 | 710 | 2900 | 630 | 300.0 | 1300 |
| Puntledge Summers | 433 | 1300 | 330.00 | 4000 | 6800 | 3800 | 12000 | 2900 | 1600.0 | 5400 |
| Nanaimo Falls | 545 | 1600 | 400.00 | 5100 | 8600 | 4800 | 15000 | 3700 | 2000.0 | 6800 |
| Klinaklini | 1475 | 4500 | 1100.00 | 14000 | 24000 | 13000 | 41000 | 10000 | 5600.0 | 18000 |
| Maria Slough | 31 | 89 | 20.00 | 310 | 460 | 210 | 1100 | 200 | 88.0 | 460 |
| Homathko | 286 | 860 | 210.00 | 2700 | 4500 | 2400 | 8300 | 1900 | 1000.0 | 3700 |
| Okanagan | 611 | 1900 | 470.00 | 5600 | 9600 | 5500 | 17000 | 4200 | 2300.0 | 7500 |
| Ahnuhati | 103 | 300 | 73.00 | 1000 | 1600 | 800 | 3200 | 690 | 340.0 | 1400 |
| Apple | 104 | 310 | 73.00 | 990 | 1600 | 800 | 3200 | 690 | 340.0 | 1400 |
| Sim | 24 | 70 | 16.00 | 250 | 370 | 160 | 850 | 160 | 67.0 | 380 |
| Franklin | 120 | 360 | 86.00 | 1200 | 1900 | 950 | 3700 | 800 | 400.0 | 1600 |
| Southgate | 179 | 530 | 130.00 | 1700 | 2800 | 1500 | 5300 | 1200 | 620.0 | 2300 |
| Kakweiken | 51 | 150 | 35.00 | 500 | 780 | 370 | 1700 | 340 | 160.0 | 730 |
| Wakeman | 305 | 910 | 230.00 | 2800 | 4800 | 2600 | 8900 | 2100 | 1100.0 | 3900 |
| Kingcome | 282 | 860 | 210.00 | 2600 | 4400 | 2400 | 8100 | 1900 | 1000.0 | 3600 |
| Orford | 38 | 110 | 25.00 | 380 | 570 | 260 | 1200 | 250 | 110.0 | 550 |
| Stafford | 21 | 60 | 13.00 | 220 | 320 | 130 | 740 | 140 | 57.0 | 330 |
| Phillips | 193 | 580 | 140.00 | 1800 | 3000 | 1600 | 5700 | 1300 | 670.0 | 2500 |
| Brem | 221 | 660 | 160.00 | 2100 | 3500 | 1900 | 6400 | 1500 | 780.0 | 2800 |
| Indian | 177 | 530 | 130.00 | 1700 | 2700 | 1500 | 5200 | 1200 | 610.0 | 2300 |
| Quatam | 147 | 440 | 110.00 | 1400 | 2300 | 1200 | 4400 | 980 | 490.0 | 1900 |
| Seymour - Georgia Strait | 55 | 160 | 38.00 | 560 | 850 | 400 | 1800 | 370 | 170.0 | 800 |
| Theodosia | 55 | 160 | 37.00 | 540 | 840 | 400 | 1800 | 360 | 170.0 | 770 |
| Toba | 450 | 1300 | 340.00 | 4200 | 7100 | 4000 | 13000 | 3100 | 1700.0 | 5600 |
| Squamish | 832 | 2500 | 640.00 | 7600 | 13000 | 7500 | 23000 | 5700 | 3200.0 | 10000 |
| Goldstream | 42 | 120 | 29.00 | 430 | 640 | 300 | 1400 | 280 | 120.0 | 620 |
| Deadman | 754 | 1000 | 250.00 | 3200 | 5400 | 2900 | 9900 | 2300 | 1200.0 | 4300 |
| Nicola | 6225 | 4100 | 1000.00 | 13000 | 22000 | 12000 | 40000 | 9300 | 4900.0 | 18000 |
| Spius | 614 | 890 | 210.00 | 2800 | 4600 | 2500 | 8600 | 2000 | 1100.0 | 3800 |
| Coldwater | 255 | 500 | 120.00 | 1600 | 2600 | 1400 | 4800 | 1100 | 590.0 | 2100 |
| Louis | 438 | 710 | 180.00 | 2200 | 3700 | 2000 | 6900 | 1600 | 840.0 | 3000 |
| Bonaparte | 3002 | 2600 | 630.00 | 8000 | 13000 | 7100 | 25000 | 5800 | 3000.0 | 11000 |
| Bessette | 232 | 470 | 120.00 | 1500 | 2400 | 1300 | 4600 | 1100 | 540.0 | 2000 |
| Portage | 454 | 730 | 180.00 | 2300 | 3800 | 2000 | 7000 | 1600 | 860.0 | 3100 |
| Chilko | 2103 | 2000 | 500.00 | 6300 | 11000 | 5800 | 19000 | 4500 | 2400.0 | 8400 |
| Quesnel System (Cariboo) | 3998 | 3100 | 760.00 | 9700 | 16000 | 8700 | 30000 | 6900 | 3700.0 | 13000 |
| Nechako System (Stuart, Stellako) | 15674 | 7600 | 1900.00 | 24000 | 40000 | 21000 | 75000 | 17000 | 8800.0 | 33000 |
| Taseko | 2219 | 2100 | 530.00 | 6500 | 11000 | 5900 | 20000 | 4700 | 2500.0 | 8800 |
| Bridge | 351 | 620 | 150.00 | 2000 | 3200 | 1700 | 6000 | 1400 | 720.0 | 2600 |
| North Thompson and Tribs | 5910 | 4000 | 970.00 | 13000 | 21000 | 11000 | 39000 | 9000 | 4700.0 | 17000 |
| Upper Fraser Spring Agg | 33079 | 13000 | 3100.00 | 41000 | 66000 | 34000 | 120000 | 28000 | 14000.0 | 55000 |
| Birkenhead | 462 | 740 | 190.00 | 2400 | 3900 | 2100 | 7200 | 1700 | 890.0 | 3200 |
| Eagle | 594 | 870 | 210.00 | 2700 | 4600 | 2400 | 8400 | 2000 | 1000.0 | 3700 |
| Salmon @ Salmon Arm | 638 | 920 | 220.00 | 2900 | 4800 | 2600 | 8900 | 2100 | 1100.0 | 3900 |
| Seymour - South Thompson | 79 | 230 | 56.00 | 720 | 1200 | 620 | 2300 | 510 | 260.0 | 1000 |
| Endako | 690 | 970 | 240.00 | 3000 | 5000 | 2700 | 9300 | 2200 | 1100.0 | 4100 |
| Chilako | 1908 | 1900 | 480.00 | 5900 | 9900 | 5400 | 18000 | 4300 | 2300.0 | 7900 |
| Horsefly | 487 | 770 | 190.00 | 2400 | 4000 | 2100 | 7300 | 1700 | 900.0 | 3200 |
| Westroad, Baker, Naver, Narcosli, Cottonwood | 8681 | 5200 | 1300.00 | 16000 | 27000 | 14000 | 50000 | 12000 | 6100.0 | 22000 |
| Chilcotin (upper and lower) | 1993 | 1900 | 480.00 | 6100 | 10000 | 5500 | 19000 | 4400 | 2300.0 | 8200 |
| Driftwood | 708 | 980 | 240.00 | 3000 | 5100 | 2800 | 9400 | 2200 | 1200.0 | 4100 |
| Nadina | 919 | 1200 | 290.00 | 3700 | 6100 | 3300 | 11000 | 2600 | 1400.0 | 4900 |
| Upper Cariboo | 554 | 830 | 200.00 | 2600 | 4300 | 2400 | 8000 | 1900 | 990.0 | 3500 |
| Taseko (Spring Timing) Agg | 2218 | 2100 | 530.00 | 6500 | 11000 | 5900 | 20000 | 4700 | 2500.0 | 8700 |
| Nahatlatch | 246 | 480 | 120.00 | 1500 | 2500 | 1400 | 4700 | 1100 | 570.0 | 2100 |
| Upper Pitt | 287 | 540 | 130.00 | 1700 | 2800 | 1500 | 5300 | 1200 | 630.0 | 2300 |
| Big Silver | 421 | 690 | 170.00 | 2200 | 3600 | 1900 | 6700 | 1600 | 820.0 | 3000 |
| North Thompson Agg | 2086 | 2000 | 500.00 | 6200 | 10000 | 5700 | 19000 | 4500 | 2400.0 | 8400 |
The objective of this section is to provide comparison figures between the IWAM function’s estimates of SMSY and SREP to the Parken model estimates. The following plots have been limited to a maximum Smsy and Srep value of 25,000 in order to match those of the technical working group presentations.